Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

Hi folks, I have make somes alterations on my tools to adjust of according with best pratices of development of tools presented in [1] [2]. The repository of tools was changed for [3]. I was testing the tool of docking [4] with the command planemo t, but as the algorithm used is heuristic, the output files not have the same content that as output files example and planemo tests fails. Any suggestion to solve this problem?

[1] https://galaxy-iuc-standards.readthedocs.org/en/latest/best_practices.html [2] https://planemo.readthedocs.org/en/latest/ [3] https://github.com/leobiscassi/autodock_vina_tools [4] https://github.com/leobiscassi/autodock_vina_tools/tree/docking/tools/doc... Att. On Sat, Jan 30, 2016 at 3:44 PM Léo Biscassi <leo.biscassi(a)gmail.com <mailto:leo.biscassi@gmail.com>> wrote: Hi Bjorn, the branch model of ChemicalToolBoX is the same presented in [1]? Could guide me about it? [1] https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTING.md Att. On Mon, Dec 28, 2015 at 5:04 PM Léo Biscassi <leo.biscassi(a)gmail.com <mailto:leo.biscassi@gmail.com>> wrote: Ok, thanks! Best regards, On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning <bjoern.gruening(a)gmail.com <mailto:bjoern.gruening@gmail.com>> wrote: Am 28.12.2015 um 20:33 schrieb Léo Biscassi: > Hi, > Thanks all your attention. > Although my project is functional prototype, its current version is able to > integrate with projects. In fact, I was looking for projects like > ChemicalToolBoX because I would like to develop my tools under project that > has more options. In this way, ChemicalToolBoX is a great opportunity for > me. > Can you update the trello card with my project? Is it necessary for your > organization? I added you :) So you have all right to modify cards. Let me know if you need help with Tool development or git. This is exciting! Cheers, Bjoern > Best regards, > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning <bjoern.gruening(a)gmail.com <mailto:bjoern.gruening@gmail.com>> > wrote: > >> >> >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi: >>> Hi, >>> >>> I've found this Trello card ( >>> https://trello.com/c/2eIu6SBa/49-autodock-integration). Do you have more >>> information about it? >> >> Afaik we can not use his work as it was done for some company and he >> moved on ... so this is unfortunately no option afaik. >> >> >> >>> best, >>> >>> On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning <bjoern.gruening(a)gmail.com <mailto:bjoern.gruening@gmail.com> >>> >>> wrote: >>> >>>> Hi, >>>> >>>> yes we had some idea, but nothing materialised so far. We started with >>>> the visualisation, because this was more fun :) >>>> >>>> Have a look at this board for more ideas: >>>> https://trello.com/b/t9Wr8lSY/chemicaltoolbox >>>> >>>> Ciao, >>>> Bjoern >>>> >>>> >>>> Am 28.12.2015 um 19:29 schrieb Léo Biscassi: >>>>> Hi Bjorn, thanks for reply. >>>>> Would be great idea join forces in this project. How do you plan extend >>>>> ChemicalToolBoX with docking? I would like to know more details. >>>>> >>>>> Att. >>>>> >>>>> On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning < >> bjoern.gruening(a)gmail.com <mailto:bjoern.gruening@gmail.com> >>>>> >>>>> wrote: >>>>> >>>>>> Hi Léo, >>>>>> >>>>>> idneed we have a small community that is bringing Cheminformatics into >>>>>> the Galaxy. It's called ChemicalToolBox and is located here: >>>>>> >>>>>> https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox >>>>>> >>>>>> We have all the basic stuff for manipulating checmical structure >> files, >>>>>> fingerprint search, pharmacophore searches and so on. Also we did all >>>>>> the basic work on datatypes and packages. Our last addition was to >>>>>> integrate a PDB visulalisation (NGL) based on WebGL. This one is used >> to >>>>>> visualise our structures directly in Galaxy. >>>>>> >>>>>> We have also a trello board with more ideas and plans what we would >> like >>>>>> to add and Vina is one of the ig targets :) >>>>>> Would be great if we can join forces here! >>>>>> >>>>>> We also maintain a Galaxy Flavour (Galaxy Docker Image about >>>>>> Cheminformatics) that we would love to extend with Docking. >>>>>> >>>>>> Thanks for letting us know and looking forward to join forces here! >>>>>> Bjoern >>>>>> >>>>>> >>>>>> Am 28.12.2015 um 18:58 schrieb Léo Biscassi: >>>>>>> Hi folks, >>>>>>> >>>>>>> I've been developing Galaxy tools for docking protein-compounds. My >>>>>> docking >>>>>>> program is Autodock Vina. In [1] is my repository. >>>>>>> >>>>>>> I'm writing here for two purpose: >>>>>>> 1) Is there someone working in this way? I've found the project [2]. >>>>>>> 2) I would like to share these tools to Galaxy project. Are they >>>> welcome >>>>>>> for Galaxy project? Let me know the best practices for developing >>>> tools >>>>>> to >>>>>>> be shared in Galaxy project. >>>>>>> >>>>>>> [1] https://github.com/leobiscassi/galaxy_tools >>>>>>> [2] https://toolshed.g2.bx.psu.edu/ >>>>>>> >>>>>>> Thanks for any help. >>>>>>> >>>>>>> Att. >>>>>>> >>>>>>> >>>>>>> >>>>>>> ___________________________________________________________ >>>>>>> Please keep all replies on the list by using "reply all" >>>>>>> in your mail client. To manage your subscriptions to this >>>>>>> and other Galaxy lists, please use the interface at: >>>>>>> https://lists.galaxyproject.org/ >>>>>>> >>>>>>> To search Galaxy mailing lists use the unified search at: >>>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>>> >>>>>> >>>> >> -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi